A compressor is disclosed having a shaft seal assembly and system that allows a high-pressure compressor to settle-out at a lower pressure level during shutdown. The seal assembly may be disposed about a portion of the shaft and define a blow-down seal chamber, the seal assembly including one or more gas seals in fluid communication with the blow-down seal chamber. A blow-down line is communicably coupled to the blow-down seal chamber to reference the blow-down seal chamber to a low pressure reference, such as a separate centrifugal compressor, or the like. Referencing the blow-down seal chamber to the low pressure reference reduces the required sealing pressure of the one or more gas seals. A valve may be disposed in the blow-down line and configured to regulate a flow of process gas leakage through the blow-down line.